Fix examples (diffpy#265)

* Fix examples

* bump

Author: Sparks29032

docs/source/funcxy.rst

@@ -29,12 +29,12 @@ scaling factor ``bgscale``.
 We will showcase an example of how one would refine over the
 ``PDFGetter`` parameters using ``funcxy`` to obtain a PDF.
 
-Let's say you have a measured I(Q) with Q in angstroms of a lead
-nanoparticle (composition PbS) named ``sample.chi`` taken on a
-glass background. We want to match a target calculated PDF G(r)
+Let's say you have a measured I(Q) with Q in angstroms of
+glass (composition SiO2) named ``sample.chi`` taken on a
+kapton background. We want to match a target calculated PDF G(r)
 stored in a file named ``target.cgr``.
 Let's also say we have a measured I(Q) of the
-glass background ``background.chi``.
+kapton background ``background.chi``.
 
 .. code-block:: python
 
@@ -44,8 +44,8 @@ glass background ``background.chi``.
 
      pg = PDFGetter()
 
-     backgroundfile = loadData("background.chi")
-     composition = "PbS"
+     backgroundfile = "background.chi"
+     composition = "SiO2"
 
 
      def wrap(x, y, **kwargs):
@@ -150,7 +150,7 @@ our wavelength was ``1.11`` angstroms.
              centerY=cent_y+cent_offset_y
          )
 
-         return ai.integrate1D_ng(
+         return ai.integrate1d_ng(
                  pattern_2d,
                  npt=1000, unit="q_A^-1",
                  method="mean"

docs/source/index.rst

@@ -34,10 +34,11 @@ plotted below.
 
 There are also a few other morphing transformations in the program.
 If no morphing transformation is specified, ``diffpy.morph`` will return just
-the plotted PDFs.
+the plotted functions.
 
 Finally, we note that though ``diffpy.morph`` should work on other spectra
-that are not PDFs, it has not been extensively tested beyond the PDF.
+that are not from diffraction, it has not been extensively tested beyond 1D
+diffraction patterns and PDFs.
 
 To get started, please visit the `quickstart tutorial <quickstart.html>`__.
 For those looking to see more advanced features, you can read our

docs/source/morphpy.rst

@@ -22,7 +22,7 @@ Python Morphing Functions
        morph on the files `darkSub_rh20_C_01.gr` and `darkSub_rh20_C_44.gr` using the command-line
        command ::
 
-          diffpy.morph --scale=0.8 --smear=-0.08 --stretch=0.005 --rmin=1.5 --rmax=30 darkSub_rh20_C_01.gr darkSub_rh20_C_44.gr
+          diffpy.morph --scale=0.8 --smear=-0.08 --stretch=0.005 --xmin=1.5 --xmax=30 darkSub_rh20_C_01.gr darkSub_rh20_C_44.gr
 
     2. To do the same on Python, we must first create a new Python script in the same directory as the
        data files `darkSub_rh20_C_01.gr` and `darkSub_rh20_C_44.gr`.
@@ -32,7 +32,7 @@ Python Morphing Functions
 
     3. Finally, we run the ``morph`` function ::
 
-           morph_info, morph_table = morph("darkSub_rh20_C_01.gr", "darkSub_rh20_C_44.gr", scale=0.8, smear=-0.08, stretch=0.005, rmin=1.5, rmax=30)
+           morph_info, morph_table = morph("darkSub_rh20_C_01.gr", "darkSub_rh20_C_44.gr", scale=0.8, smear_pdf=-0.08, stretch=0.005, xmin=1.5, xmax=30)
 
        * The ``morph`` function takes in two file names (or paths). You can also provide various parameters
          for morphing (see the Full Parameter List below).
@@ -62,7 +62,7 @@ Python Morphing Functions
        `darkSub_rh20_C_44.gr` into ``ds_rh20_c_44_array``, we can apply the same morph as step 3
        by running ::
 
-           morph_info, morph_table = morph_arrays(ds_rh20_c_01_array, ds_rh20_c_44_array, scale=0.8, smear=-0.08, stretch=0.5, rmin=1.5, rmax=30)
+           morph_info, morph_table = morph_arrays(ds_rh20_c_01_array, ds_rh20_c_44_array, scale=0.8, smear_pdf=-0.08, stretch=0.5, xmin=1.5, xmax=30)
 
     9. Notice that the two-column format of the input to ``morph_arrays`` is the same as the
        output of ``morph`` and ``morph_arrays``. It is VERY IMPORTANT that the data is in two-column format
@@ -86,9 +86,9 @@ get_diff: bool
 verbose: bool
     Print additional header details to saved files. These include details about the morph
     inputs and outputs.
-rmin: float
+xmin: float
     Minimum r-value (abscissa) to use for function comparisons.
-rmax: float
+xmax: float
     Maximum r-value (abscissa) to use for function comparisons.
 tolerance: float
     Specify least squares refiner tolerance when optimizing for morph parameters. Default: 10e-8.

docs/source/quickstart.rst

@@ -148,7 +148,7 @@ Basic diffpy.morph Workflow
     7. Now, we will examine the Gaussian smearing factor. We provide an
        initial guess by typing ::
 
-           diffpy.morph --scale=0.8 --smear=0.5 -a darkSub_rh20_C_01.gr darkSub_rh20_C_44.gr
+           diffpy.morph --scale=0.8 --smear-pdf=0.5 -a darkSub_rh20_C_01.gr darkSub_rh20_C_44.gr
 
        And viewing the results. We've tailored our scale factor to be
        close to the value given by ``diffpy.morph``, but see that the difference
@@ -162,17 +162,17 @@ Basic diffpy.morph Workflow
          superficial and in most cases can be ignored.
 
        We see that this has had hardly any effect on our PDF. To see
-       an effect, we restrict the ``rmin`` and ``rmax`` values to
+       an effect, we restrict the ``xmin`` and ``xmax`` values to
        reflect relevant data range by typing ::
 
-           diffpy.morph --scale=0.8 --smear=0.5 --rmin=1.5 --rmax=30 darkSub_rh20_C_01.gr darkSub_rh20_C_44.gr
+           diffpy.morph --scale=0.8 --smear-pdf=0.5 --xmin=1.5 --xmax=30 darkSub_rh20_C_01.gr darkSub_rh20_C_44.gr
 
        Now, we see that the difference Rw = 0.204 and that the optimized
        ``smear=-0.084138``.
 
-       * We restricted the r values because some of the Gaussian
-         smear effects are only visible in a fixed r range. We
-         chose this r range by noting where most of our relevant
+       * We restricted the ``x``-axis (``r``) values because some of the Gaussian
+         smear effects are only visible in a fixed ``x`` range. We
+         chose this ``x`` range by noting where most of our relevant
          data was that was not exponentially decayed by
          instrumental shortcomings.
 
@@ -181,7 +181,7 @@ Basic diffpy.morph Workflow
     8. Finally, we will examine the stretch factor. Provide an initial
        guess by typing ::
 
-           diffpy.morph --scale=0.8 --smear=-0.08 --stretch=0.005 --rmin=1.5 --rmax=30 -a darkSub_rh20_C_01.gr darkSub_rh20_C_44.gr
+           diffpy.morph --scale=0.8 --smear-pdf=-0.08 --stretch=0.005 --xmin=1.5 --xmax=30 -a darkSub_rh20_C_01.gr darkSub_rh20_C_44.gr
 
        And noting that the difference has increased. Before continuing,
        see if you can see which direction (higher or lower) our initial
@@ -190,7 +190,7 @@ Basic diffpy.morph Workflow
 
        If you cannot, type ::
 
-           diffpy.morph --scale=0.8 --smear=-0.08 --stretch=0.005 --rmin=1.5 --rmax=30 -a darkSub_rh20_C_01.gr darkSub_rh20_C_44.gr
+           diffpy.morph --scale=0.8 --smear-pdf=-0.08 --stretch=0.005 --xmin=1.5 --xmax=30 -a darkSub_rh20_C_01.gr darkSub_rh20_C_44.gr
 
        to observe decreased difference and then remove ``-a`` to see
        the optimized ``--stretch=0.001762``. We have now reached

docs/source/tutorials.rst

@@ -179,7 +179,8 @@ files can be found in ``additionalData/morphsqueeze/``.
 .. warning::
 
    **Extrapolation risk:**
-   A polynomial squeeze can shift morph data outside the target’s ``r``-range,
+   A polynomial squeeze can shift morph data outside the target’s grid
+   (``x``-axis) range,
    so parts of the output may be extrapolated.
    This is generally fine if the polynomial coefficients are small and
    the distortion is therefore small. If your coefficients are large, check the
@@ -236,12 +237,12 @@ Currently, the supported nanoparticle shapes include: spheres and spheroids.
         3. Now, we are ready to perform a morph applying spherical
 	   effects. To do so, we use the ``--radius`` parameter ::
 
-               diffpy.morph Ni_bulk.gr Ni_nano_sphere.cgr --radius=11.2 -a --rmax=30
+               diffpy.morph Ni_bulk.gr Ni_nano_sphere.cgr --radius=11.2 -a --xmax=30
 
         4. We can see that the :math:`Rw` value has significantly decreased
 	   from before. Run without the ``-a`` tag to refine ::
 
-               diffpy.morph Ni_bulk.gr Ni_nano_sphere.cgr --radius=11.2 --rmax=30
+               diffpy.morph Ni_bulk.gr Ni_nano_sphere.cgr --radius=11.2 --xmax=30
 
         5. After refining, we see the actual radius of the
 	   nanoparticle was closer to 12.
@@ -259,13 +260,13 @@ Currently, the supported nanoparticle shapes include: spheres and spheroids.
 	   enough information to define our spheroid. To apply
 	   spheroid shape effects onto our bulk, run ::
 
-               diffpy.morph Ni_bulk.gr Ni_nano_spheroid.cgr --radius=12 --pradius=6 -a --rmax=30
+               diffpy.morph Ni_bulk.gr Ni_nano_spheroid.cgr --radius=12 --pradius=6 -a --xmax=30
 
            Note that the equatorial radius corresponds to the
 	   ``--radius`` parameter and polar radius to ``--pradius``.
 
         3. Remove the ``-a`` tag to refine.
 
 There is also support for morphing from a nanoparticle to a bulk. When
-applying the inverse morphs, it is recommended to set ``--rmax=psize``
+applying the inverse morphs, it is recommended to set ``--xmax=psize``
 where ``psize`` is the longest diameter of the nanoparticle.

news/example_fix.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Tutorial examples for funcxy and pyfai now run properly.
+
+**Security:**
+
+* <news item>